Optimised PDB entry 4jv5



Structure
SpacegroupP 41 21 2
Cell dimensionsa: 401.000 Åb: 401.000 Åc: 176.000 Å
α: 90.00°β: 90.00°γ: 90.00°
Resolution3.16 Å

Experimental data
ReflectionsAll: 231145Test set: 11558 (5.0%)
Resolution range29.88 Å3.16 Å

R-values etc.
From PDB headerCalculated from dataAfter re-refinementAfter re-refinement and rebuilding
R0.19700.19800.19250.1916
R-free0.24900.24870.23550.2346
σR-free 0.00230.00220.0022
Z(R-free) -4.83-2.05-2.14

WHAT_CHECK validation
Original PDB entryRe-refined (only)Re-refined and rebuilt
1st generation packing quality1-2.331-2.075-2.058
2nd generation packing quality1-3.228-2.854-2.866
Ramachandran plot appearance1-5.633-4.483-4.234
Chi-1/Chi-2 rotamer normality1-6.226-5.220-4.480
Backbone conformation1-0.2520.2350.332
Bond length RMS Z-score20.4990.4530.454
Bond angle RMS Z-score20.9000.8450.844
Total number of bumps31745922944
Unsatisfied H-bond donors/acceptors30396378
LinkLinkLink

1 Higher is better, 2 Should be lower than 1.000, 3 Fewer is better


Density map fit (real-space correlation coefficient)
Significantly improved residues139
Significantly deteriorated residues40
Changes of all residuesPlot

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